Background: Thymic epithelial tumors (TETs) are rare and biologically heterogeneous. As Hippo pathway dysregulation can manifest through altered YAP/TEAD-dependent transcription and compartment-specific protein distribution, we integrated RT-qPCR and immunohistochemistry (IHC) to identify coordinated expression and localization patterns within the YAP–TEAD axis. Methods: In formalin-fixed, paraffin-embedded (FFPE) TET samples, MST1, SAV1, LATS1, MOB1A, YAP1, and TEAD4 were quantified by RT-qPCR using the 2^-ΔΔCq method relative to pooled normal. IHC was scored separately for nuclear and cytoplasmic positivity and staining intensity. Associations between mRNA and IHC were assessed using Spearman correlation. Principal component analysis (PCA) was conducted, and sampling adequacy was evaluated using the Kaiser–Meyer–Olkin (KMO) measure. The PCA model (overall KMO = 0.71) included mRNA expression and nuclear/cytoplasmic IHC of YAP1, phosphorylated YAP (AYAP), and TEAD4. Results: No significant mRNA–protein associations were observed for upstream markers (MST1, SAV1, LATS1, MOB1A; all p > 0.05). In contrast, YAP1 mRNA positively correlated with cytoplasmic (R = 0.49, p = 0.016) and nuclear YAP1 positivity (R = 0.47, p = 0.024). AYAP showed the strongest coupling between mRNA and protein readouts (cytoplasmic R = 0.60, p = 0.002; nuclear R = 0.49, p = 0.017). TEAD4 mRNA correlated with cytoplasmic TEAD4 positivity (R = 0.45, p = 0.032) but not with nuclear TEAD4 (R = 0.29, p = 0.182). PCA PC1 captured coordinated overall variation across mRNA and protein compartments, whereas PC2 reflected a contrast between TEAD4 transcript/cytoplasmic TEAD4 and nuclear YAP/AYAP patterns. Type A thymomas tended toward higher PC1, B1/B2 toward lower PC1, B3 displayed heterogeneity, and thymic carcinomas shifted predominantly along PC2. Conclusion: Downstream effectors (YAP1/TEAD4) show stronger mRNA–protein concordance than upstream Hippo components. Integrative PCA reveals subtype-associated YAP–TEAD signaling states and supports compartment-resolved profiling as a complementary biomarker strategy in TETs.